This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, the human COQ3 enzyme can restore biosynthesis of ubiquinone-6 in coq3 deletion mutants of yeast [3].
The enzymes from yeast, Escherichia coli and rat also catalyse the methylation of 3,4-dihydroxy-5-all-trans-polyprenylbenzoate [3] (a reaction that is classified as EC 2.1.1.114, polyprenyldihydroxybenzoate methyltransferase).